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Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with IP5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XAM PDB ENTRY 2XAM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.9 22% PEG 3300, 100 MM BIS-TRIS PH 5.9, 2 MM MGCL2. PROTEIN WAS MIXED WITH 2 MM INOSITOL-5-P
Crystal Properties Matthews coefficient Solvent content 2.3 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.761 α = 90 b = 112.737 β = 90 c = 144.454 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.7 88.74 100 0.13 4.24 6.92 22033 2 57
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.06 100 0.45 1.66 6.99
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2XAM 2.9 88.736 21980 1141 99.995 0.228 0.2249 0.2907 0.2596 RANDOM 38.993
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.267 -1.716 1.449
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.168 r_dihedral_angle_3_deg 20.117 r_dihedral_angle_4_deg 19.598 r_dihedral_angle_1_deg 5.543 r_scangle_it 1.847 r_angle_refined_deg 1.371 r_scbond_it 1.067 r_mcangle_it 0.937 r_mcbond_it 0.524 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.168 r_dihedral_angle_3_deg 20.117 r_dihedral_angle_4_deg 19.598 r_dihedral_angle_1_deg 5.543 r_scangle_it 1.847 r_angle_refined_deg 1.371 r_scbond_it 1.067 r_mcangle_it 0.937 r_mcbond_it 0.524 r_nbtor_refined 0.306 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.215 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.09 r_symmetry_hbond_refined 0.086 r_metal_ion_refined 0.063 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6602 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling